DB code: S00413

RLCP classification 3.113.90000.331 : Transfer
3.1143.50000.64 : Transfer
CATH domain 3.30.930.10 : BirA Bifunctional Protein; domain 2 Catalytic domain
E.C. 6.3.1.1
CSA 12as
M-CSA 12as
MACiE M0075

CATH domain Related DB codes (homologues)
3.30.930.10 : BirA Bifunctional Protein; domain 2 D00291 D00293 D00294 D00295 M00049 T00113

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P00963 Aspartate--ammonia ligase
EC 6.3.1.1
Asparagine synthetase A
NP_418200.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_006952153.1 (Protein)
NC_019049.1 (DNA/RNA sequence)
YP_491685.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF03590 (AsnA)
[Graphical View]

KEGG enzyme name
aspartate---ammonia ligase
asparagine synthetase
L-asparagine synthetase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P00963 ASNA_ECOLI ATP + L-aspartate + NH(3) = AMP + diphosphate + L-asparagine. Homodimer. Cytoplasm.

KEGG Pathways
Map code Pathways E.C.
MAP00252 Alanine and aspartate metabolism
MAP00460 Cyanoamino acid metabolism
MAP00910 Nitrogen metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00002 C00049 C00014 C00020 C00013 C00152
E.C.
Compound Magnesium ATP L-Aspartate NH3 AMP Pyrophosphate L-Asparagine
Type divalent metal (Ca2+, Mg2+) amine group,nucleotide amino acids,carboxyl group amine group,organic ion amine group,nucleotide phosphate group/phosphate ion amino acids,amide group
ChEBI 18420
 18420
 		15422
 15422
 		17053
 17053
 		16134
 16134
 		16027
 16027
 		29888
 29888
 		17196
 58048
 17196
 58048
PubChem 888
 888
 		5957
 5957
 		44367445
 5960
 44367445
 5960
 		222
 222
 		6083
 6083
 		1023
 21961011
 1023
 21961011
 		6267
 6992089
 6267
 6992089
11asA Unbound Unbound Unbound Unbound Unbound Unbound Bound:ASN
11asB Unbound Unbound Unbound Unbound Unbound Unbound Bound:ASN
12asA Unbound Unbound Unbound Unbound Bound:AMP Unbound Bound:ASN
12asB Unbound Unbound Unbound Unbound Bound:AMP Unbound Bound:ASN

Reference for Active-site residues
resource references E.C.
literature [5] & [6]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
11asA ASP 46;ARG 100;GLN 116 ASP 235;GLU 248(magnesium binding) mutant C51A, C315A
11asB ASP 46;ARG 100;GLN 116 ASP 235;GLU 248(magnesium binding) mutant C51A, C315A
12asA ASP 46;ARG 100;GLN 116 ASP 235;GLU 248(magnesium binding) mutant C51A, C315A
12asB ASP 46;ARG 100;GLN 116 ASP 235;GLU 248(magnesium binding) mutant C51A, C315A

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[5]
p.16
[6]
Scheme 1, p.5800 3

References
[1]
Resource
Comments
Medline ID
PubMed ID 22754
Journal J Med Chem
Year 1978
Volume 21
Pages 45-9
Authors Brynes S, Burckart GJ, Mokotoff M
Title Potential inhibitors of L-asparagine biosynthesis. 4. Substituted sulfonamide and sulfonylhydrazide analogues of L-asparagine.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 2858178
Journal Arch Biochem Biophys
Year 1985
Volume 237
Pages 335-46
Authors Luehr CA, Schuster SM
Title Purification and characterization of beef pancreatic asparagine synthetase.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 1346128
Journal J Biol Chem
Year 1992
Volume 267
Pages 144-9
Authors Hinchman SK, Henikoff S, Schuster SM
Title A relationship between asparagine synthetase A and aspartyl tRNA synthetase.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 9559053
Journal Adv Enzymol Relat Areas Mol Biol
Year 1998
Volume 72
Pages 145-98
Authors Richards NG, Schuster SM
Title Mechanistic issues in asparagine synthetase catalysis.
Related PDB
Related UniProtKB
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS)
Medline ID 98100076
PubMed ID 9437423
Journal Nat Struct Biol
Year 1998
Volume 5
Pages 15-9
Authors Nakatsu T, Kato H, Oda J
Title Crystal structure of asparagine synthetase reveals a close evolutionary relationship to class II aminoacyl-tRNA synthetase.
Related PDB 11as 12as
Related UniProtKB P00963
[6]
Resource
Comments
Medline ID
PubMed ID
Journal J Am Chem Soc
Year 1999
Volume 121
Pages 5799-800
Authors Koizumi M, Hiratake J, Nakatsu T, Kato H, Oda J,
Title A Potent Transition-State Analogue Inhibitor of Escherichia coli Asparagine Synthetase A
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 10948265
Journal Plant Cell
Year 2000
Volume 12
Pages 1491-509
Authors Wang R, Guegler K, LaBrie ST, Crawford NM
Title Genomic analysis of a nutrient response in Arabidopsis reveals diverse expression patterns and novel metabolic and potential regulatory genes induced by nitrate.
Related PDB
Related UniProtKB

Comments
Asparagine synthase A (S00413) catalyzes NH3-dependent activity, whilst asparagine synthase B (E.C. 6.3.5.4; D00300) catalyzes glutamine-dependent activity.
According to the literature [5] & [6], this enzyme catalyzes two successive transfer reactions. Firstly, this enzyme transfers adenylate from ATP to the beta-carboxylate of another substrate, L-aspartate forming an intermediate, beta-aspartyl adenylate. Secondly, it transfers acyl group of the intermediate to ammonia (NH3), releasing diphosphate.
The first reaction (adenylate transfer) proceeds as follows (see [5] & [6]):
(1) The acceptor group, the beta-carboxylate oxygen atom of the substrate, L-aspartate, makes a nucleophilic attack on the transferred group, the phosphorus atom of the alpha-phosphate group of ATP. At this step, Gln116 seems to stabilize the acceptor, the beta-carboxylate.
(2) Arg100 stabilizes the transferred group, the alpha-phosphate of ATP, whereas Arg299 and magnesium ion bound to Asp235 and Glu248 stabilize the leaving group, the beta- and gamma-phosphate groups of ATP.
(3) The leaving group, the diphosphate will be released.
The second reaction (acyl transfer) proceeds as follows (see [5] & [6]):
(1') The acceptor group, ammonia, makes a nucleophilic attack on the carbonyl carbon of the adenylated aspartate intermediate, forming a tetrahedral oxyanion transtion-state or intermediate, which has a zwitterionic character.
(2') Arg106 and Gln116 stabilize the negative charge on the oxyanion part of the transition-state or intermediate, whilst Asp46 stabilizes the positive charge on the -NH3(+) part.
(3') Asp46 acts as a general base, to deprotonate the -NH3 group of the transition-state/intermediate, releasing the leaving group, adenylate (AMP).

Created Updated
2004-08-01 2009-02-26